MCL coexpression mm9:2596: Difference between revisions
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{{MCL_coexpression_mm9| | 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vesicle membrane;0.0360765078419499;27204!GO:0051649;establishment of cellular localization;0.0360765078419499;27204,16564!GO:0051641;cellular localization;0.0360765078419499;27204,16564!GO:0005871;kinesin complex;0.0360765078419499;16564!GO:0005524;ATP binding;0.0360765078419499;27204,16564!GO:0032559;adenyl ribonucleotide binding;0.0360765078419499;27204,16564!GO:0030554;adenyl nucleotide binding;0.0360765078419499;27204,16564!GO:0044433;cytoplasmic vesicle part;0.0360765078419499;27204!GO:0007269;neurotransmitter secretion;0.0360765078419499;27204!GO:0008021;synaptic vesicle;0.0360765078419499;27204!GO:0012506;vesicle membrane;0.0360765078419499;27204!GO:0045055;regulated secretory pathway;0.0360765078419499;27204!GO:0003777;microtubule motor activity;0.0360765078419499;16564!GO:0032553;ribonucleotide binding;0.0360765078419499;27204,16564!GO:0032555;purine ribonucleotide binding;0.0360765078419499;27204,16564!GO:0017076;purine nucleotide binding;0.0360765078419499;27204,16564!GO:0030136;clathrin-coated vesicle;0.0360765078419499;27204!GO:0007018;microtubule-based movement;0.0360765078419499;16564!GO:0003001;generation of a signal involved in cell-cell signaling;0.0360765078419499;27204!GO:0030135;coated vesicle;0.0360765078419499;27204!GO:0001505;regulation of neurotransmitter levels;0.0360765078419499;27204!GO:0000166;nucleotide binding;0.0360765078419499;27204,16564!GO:0030705;cytoskeleton-dependent intracellular transport;0.0366866860417446;16564!GO:0005875;microtubule associated complex;0.0366866860417446;16564!GO:0006810;transport;0.0439919398657478;27204,16564!GO:0044446;intracellular organelle part;0.0439919398657478;27204,16564!GO:0044422;organelle part;0.0439919398657478;27204,16564!GO:0016043;cellular component organization and biogenesis;0.0439919398657478;27204,16564!GO:0051234;establishment of localization;0.0439919398657478;27204,16564!GO:0045045;secretory pathway;0.0464001961037806;27204!GO:0007017;microtubule-based process;0.0464001961037806;16564!GO:0016023;cytoplasmic membrane-bound vesicle;0.0464001961037806;27204!GO:0051179;localization;0.0464001961037806;27204,16564!GO:0007268;synaptic transmission;0.0464001961037806;27204!GO:0005874;microtubule;0.0464001961037806;16564!GO:0031988;membrane-bound vesicle;0.0464001961037806;27204!GO:0032940;secretion by cell;0.0479228385937083;27204!|ontology_enrichment_celltype=CL:0000540!4.91e-17!33;CL:0000047!4.91e-17!33;CL:0000031!4.91e-17!33;CL:0000404!4.91e-17!33;CL:0000393!1.57e-11!39;CL:0000211!1.57e-11!39;CL:0000117!3.60e-11!23;CL:0000337!3.60e-11!23;CL:0000221!4.64e-09!44;CL:0000133!4.64e-09!44;CL:0002319!1.00e-08!43|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0001017!1.32e-24!73;UBERON:0004121!1.31e-23!95;UBERON:0000924!1.31e-23!95;UBERON:0006601!1.31e-23!95;UBERON:0001016!2.46e-23!75;UBERON:0002346!6.44e-22!64;UBERON:0003075!6.44e-22!64;UBERON:0007284!6.44e-22!64;UBERON:0010371!5.83e-21!73;UBERON:0000073!5.01e-19!54;UBERON:0001049!8.12e-18!52;UBERON:0005068!8.12e-18!52;UBERON:0006241!8.12e-18!52;UBERON:0007135!8.12e-18!52;UBERON:0003056!2.78e-16!49;UBERON:0000955!2.59e-15!47;UBERON:0006238!2.59e-15!47;UBERON:0002616!9.33e-15!46;UBERON:0003080!2.98e-14!40;UBERON:0002020!8.87e-14!34;UBERON:0002780!1.37e-13!39;UBERON:0001890!1.37e-13!39;UBERON:0006240!1.37e-13!39;UBERON:0003528!1.65e-11!29;UBERON:0002791!1.65e-11!29;UBERON:0001893!1.65e-11!29;UBERON:0010314!4.38e-11!92;UBERON:0000956!9.23e-08!21;UBERON:0001869!9.23e-08!21;UBERON:0000203!9.23e-08!21;UBERON:0000489!4.53e-07!21;UBERON:0002021!5.36e-07!10;UBERON:0000411!5.36e-07!10;UBERON:0001950!5.36e-07!10|tfbs_overrepresentation_for_novel_motifs=0.752782,0.564138,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,0.870507,0.906098,1.18012,0.933025,0.608226,0,1.14208,0.578045,1.138,0.876292,0.679146,0.756749,0.932027,0.585919,0.731217,0.963352,1.1146,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.872889,0.563758,2.08624,1.32715,0.50014,0.582863,0.831295,0.724277,0.610669,0.922882,0.788421,1.05665,0.859154,0.663409,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,1.23806,1.11142,2.19064,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.777706,1.44925,1.882,2.7424,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.535545,0.195254,0.99201,1.06194,2.07346,1.62608,1.33496,1.26245,1.4508,2.26459,0.509215,1.17262,1.26539,1.05692,2.50519,1.38502,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,2.53104,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,1.862,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.999018,2.0485,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,1.75703,1.11251,0.94678,0.562367,0.904334,0.833542|tfbs_overrepresentation_jaspar=MA0003.1;0.245953,MA0004.1;0.801718,MA0006.1;0.60285,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;0.825079,MA0017.1;0.635031,MA0019.1;1.08369,MA0024.1;1.23079,MA0025.1;1.51835,MA0027.1;2.9431,MA0028.1;0.61552,MA0029.1;1.20789,MA0030.1;1.21482,MA0031.1;1.17722,MA0038.1;0.963265,MA0040.1;1.28983,MA0041.1;0.714279,MA0042.1;0.69885,MA0043.1;1.3775,MA0046.1;1.31428,MA0048.1;0.353763,MA0050.1;0.845669,MA0051.1;0.973068,MA0052.1;1.29825,MA0055.1;0.190475,MA0056.1;0,MA0057.1;0.896032,MA0058.1;0.690848,MA0059.1;0.705317,MA0060.1;2.1699,MA0061.1;0.5406,MA0063.1;0,MA0066.1;0.951196,MA0067.1;1.63197,MA0068.1;0.343188,MA0069.1;1.29861,MA0070.1;1.28847,MA0071.1;0.844726,MA0072.1;1.2796,MA0073.1;0.439282,MA0074.1;0.911576,MA0076.1;0.657929,MA0077.1;1.2569,MA0078.1;1.0091,MA0081.1;0.732313,MA0083.1;1.37668,MA0084.1;1.96428,MA0087.1;1.33189,MA0088.1;0.27999,MA0089.1;0,MA0090.1;0.762482,MA0091.1;0.816659,MA0092.1;0.762845,MA0093.1;0.62555,MA0095.1;0,MA0098.1;0,MA0100.1;0.89873,MA0101.1;0.71579,MA0103.1;0.647985,MA0105.1;0.405648,MA0106.1;1.01755,MA0107.1;0.640607,MA0108.2;1.10817,MA0109.1;0,MA0111.1;0.778753,MA0113.1;0.986839,MA0114.1;1.3296,MA0115.1;1.38041,MA0116.1;0.602598,MA0117.1;1.34691,MA0119.1;0.716476,MA0122.1;1.36752,MA0124.1;1.57762,MA0125.1;1.5017,MA0130.1;0,MA0131.1;1.07881,MA0132.1;0,MA0133.1;0,MA0135.1;1.4152,MA0136.1;0.933582,MA0139.1;1.16863,MA0140.1;0.898603,MA0141.1;0.671467,MA0142.1;1.16183,MA0143.1;1.00467,MA0144.1;0.541532,MA0145.1;0.292366,MA0146.1;0.151124,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;0.412742,MA0035.2;0.903829,MA0039.2;1.10518,MA0138.2;1.07027,MA0002.2;0.466067,MA0137.2;0.668025,MA0104.2;0.48458,MA0047.2;0.962424,MA0112.2;0.29236,MA0065.2;1.44804,MA0150.1;0.784464,MA0151.1;0,MA0152.1;0.962542,MA0153.1;1.43238,MA0154.1;1.65374,MA0155.1;0.840842,MA0156.1;0.656895,MA0157.1;1.12772,MA0158.1;0,MA0159.1;0.569393,MA0160.1;0.823568,MA0161.1;0,MA0162.1;1.53682,MA0163.1;2.12767,MA0164.1;2.15144,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;1.4764,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0}} | ||
Latest revision as of 18:47, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr10:85961581..85961603,- | p2@Syn3 |
| Mm9::chr10:85961617..85961654,- | p1@Syn3 |
| Mm9::chr15:90880254..90880298,- | p1@Kif21a |
Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data
| GO ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0030672 | synaptic vesicle membrane | 0.0360765078419499 |
| GO:0051649 | establishment of cellular localization | 0.0360765078419499 |
| GO:0051641 | cellular localization | 0.0360765078419499 |
| GO:0005871 | kinesin complex | 0.0360765078419499 |
| GO:0005524 | ATP binding | 0.0360765078419499 |
| GO:0032559 | adenyl ribonucleotide binding | 0.0360765078419499 |
| GO:0030554 | adenyl nucleotide binding | 0.0360765078419499 |
| GO:0044433 | cytoplasmic vesicle part | 0.0360765078419499 |
| GO:0007269 | neurotransmitter secretion | 0.0360765078419499 |
| GO:0008021 | synaptic vesicle | 0.0360765078419499 |
| GO:0012506 | vesicle membrane | 0.0360765078419499 |
| GO:0045055 | regulated secretory pathway | 0.0360765078419499 |
| GO:0003777 | microtubule motor activity | 0.0360765078419499 |
| GO:0032553 | ribonucleotide binding | 0.0360765078419499 |
| GO:0032555 | purine ribonucleotide binding | 0.0360765078419499 |
| GO:0017076 | purine nucleotide binding | 0.0360765078419499 |
| GO:0030136 | clathrin-coated vesicle | 0.0360765078419499 |
| GO:0007018 | microtubule-based movement | 0.0360765078419499 |
| GO:0003001 | generation of a signal involved in cell-cell signaling | 0.0360765078419499 |
| GO:0030135 | coated vesicle | 0.0360765078419499 |
| GO:0001505 | regulation of neurotransmitter levels | 0.0360765078419499 |
| GO:0000166 | nucleotide binding | 0.0360765078419499 |
| GO:0030705 | cytoskeleton-dependent intracellular transport | 0.0366866860417446 |
| GO:0005875 | microtubule associated complex | 0.0366866860417446 |
| GO:0006810 | transport | 0.0439919398657478 |
| GO:0044446 | intracellular organelle part | 0.0439919398657478 |
| GO:0044422 | organelle part | 0.0439919398657478 |
| GO:0016043 | cellular component organization and biogenesis | 0.0439919398657478 |
| GO:0051234 | establishment of localization | 0.0439919398657478 |
| GO:0045045 | secretory pathway | 0.0464001961037806 |
| GO:0007017 | microtubule-based process | 0.0464001961037806 |
| GO:0016023 | cytoplasmic membrane-bound vesicle | 0.0464001961037806 |
| GO:0051179 | localization | 0.0464001961037806 |
| GO:0007268 | synaptic transmission | 0.0464001961037806 |
| GO:0005874 | microtubule | 0.0464001961037806 |
| GO:0031988 | membrane-bound vesicle | 0.0464001961037806 |
| GO:0032940 | secretion by cell | 0.0479228385937083 |
Relative expression of the co-expression cluster over median <br>Analyst:
Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>
| Ontology term | p-value | n |
|---|---|---|
| neuron | 4.91e-17 | 33 |
| neuronal stem cell | 4.91e-17 | 33 |
| neuroblast | 4.91e-17 | 33 |
| electrically signaling cell | 4.91e-17 | 33 |
| electrically responsive cell | 1.57e-11 | 39 |
| electrically active cell | 1.57e-11 | 39 |
| CNS neuron (sensu Vertebrata) | 3.60e-11 | 23 |
| neuroblast (sensu Vertebrata) | 3.60e-11 | 23 |
| ectodermal cell | 4.64e-09 | 44 |
| neurectodermal cell | 4.64e-09 | 44 |
| neural cell | 1.00e-08 | 43 |
| Ontology term | p-value | n |
|---|---|---|
| central nervous system | 1.32e-24 | 73 |
| ectoderm-derived structure | 1.31e-23 | 95 |
| ectoderm | 1.31e-23 | 95 |
| presumptive ectoderm | 1.31e-23 | 95 |
| nervous system | 2.46e-23 | 75 |
| neurectoderm | 6.44e-22 | 64 |
| neural plate | 6.44e-22 | 64 |
| presumptive neural plate | 6.44e-22 | 64 |
| ecto-epithelium | 5.83e-21 | 73 |
| regional part of nervous system | 5.01e-19 | 54 |
| neural tube | 8.12e-18 | 52 |
| neural rod | 8.12e-18 | 52 |
| future spinal cord | 8.12e-18 | 52 |
| neural keel | 8.12e-18 | 52 |
| pre-chordal neural plate | 2.78e-16 | 49 |
| brain | 2.59e-15 | 47 |
| future brain | 2.59e-15 | 47 |
| regional part of brain | 9.33e-15 | 46 |
| anterior neural tube | 2.98e-14 | 40 |
| gray matter | 8.87e-14 | 34 |
| regional part of forebrain | 1.37e-13 | 39 |
| forebrain | 1.37e-13 | 39 |
| future forebrain | 1.37e-13 | 39 |
| brain grey matter | 1.65e-11 | 29 |
| regional part of telencephalon | 1.65e-11 | 29 |
| telencephalon | 1.65e-11 | 29 |
| structure with developmental contribution from neural crest | 4.38e-11 | 92 |
| cerebral cortex | 9.23e-08 | 21 |
| cerebral hemisphere | 9.23e-08 | 21 |
| pallium | 9.23e-08 | 21 |
| cavitated compound organ | 4.53e-07 | 21 |
| occipital lobe | 5.36e-07 | 10 |
| visual cortex | 5.36e-07 | 10 |
| neocortex | 5.36e-07 | 10 |
TFBS overrepresentation<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data
Novel motifs
JASPAR motifs
| Motifs | -log10(p-value) |
|---|---|
| MA0003.1 | 0.245953 |
| MA0004.1 | 0.801718 |
| MA0006.1 | 0.60285 |
| MA0007.1 | 0.784593 |
| MA0009.1 | 1.27673 |
| MA0014.1 | 0.825079 |
| MA0017.1 | 0.635031 |
| MA0019.1 | 1.08369 |
| MA0024.1 | 1.23079 |
| MA0025.1 | 1.51835 |
| MA0027.1 | 2.9431 |
| MA0028.1 | 0.61552 |
| MA0029.1 | 1.20789 |
| MA0030.1 | 1.21482 |
| MA0031.1 | 1.17722 |
| MA0038.1 | 0.963265 |
| MA0040.1 | 1.28983 |
| MA0041.1 | 0.714279 |
| MA0042.1 | 0.69885 |
| MA0043.1 | 1.3775 |
| MA0046.1 | 1.31428 |
| MA0048.1 | 0.353763 |
| MA0050.1 | 0.845669 |
| MA0051.1 | 0.973068 |
| MA0052.1 | 1.29825 |
| MA0055.1 | 0.190475 |
| MA0056.1 | 0 |
| MA0057.1 | 0.896032 |
| MA0058.1 | 0.690848 |
| MA0059.1 | 0.705317 |
| MA0060.1 | 2.1699 |
| MA0061.1 | 0.5406 |
| MA0063.1 | 0 |
| MA0066.1 | 0.951196 |
| MA0067.1 | 1.63197 |
| MA0068.1 | 0.343188 |
| MA0069.1 | 1.29861 |
| MA0070.1 | 1.28847 |
| MA0071.1 | 0.844726 |
| MA0072.1 | 1.2796 |
| MA0073.1 | 0.439282 |
| MA0074.1 | 0.911576 |
| MA0076.1 | 0.657929 |
| MA0077.1 | 1.2569 |
| MA0078.1 | 1.0091 |
| MA0081.1 | 0.732313 |
| MA0083.1 | 1.37668 |
| MA0084.1 | 1.96428 |
| MA0087.1 | 1.33189 |
| MA0088.1 | 0.27999 |
| MA0089.1 | 0 |
| MA0090.1 | 0.762482 |
| MA0091.1 | 0.816659 |
| MA0092.1 | 0.762845 |
| MA0093.1 | 0.62555 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.89873 |
| MA0101.1 | 0.71579 |
| MA0103.1 | 0.647985 |
| MA0105.1 | 0.405648 |
| MA0106.1 | 1.01755 |
| MA0107.1 | 0.640607 |
| MA0108.2 | 1.10817 |
| MA0109.1 | 0 |
| MA0111.1 | 0.778753 |
| MA0113.1 | 0.986839 |
| MA0114.1 | 1.3296 |
| MA0115.1 | 1.38041 |
| MA0116.1 | 0.602598 |
| MA0117.1 | 1.34691 |
| MA0119.1 | 0.716476 |
| MA0122.1 | 1.36752 |
| MA0124.1 | 1.57762 |
| MA0125.1 | 1.5017 |
| MA0130.1 | 0 |
| MA0131.1 | 1.07881 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.4152 |
| MA0136.1 | 0.933582 |
| MA0139.1 | 1.16863 |
| MA0140.1 | 0.898603 |
| MA0141.1 | 0.671467 |
| MA0142.1 | 1.16183 |
| MA0143.1 | 1.00467 |
| MA0144.1 | 0.541532 |
| MA0145.1 | 0.292366 |
| MA0146.1 | 0.151124 |
| MA0147.1 | 0.556853 |
| MA0148.1 | 0.820161 |
| MA0149.1 | 0.722227 |
| MA0062.2 | 0.412742 |
| MA0035.2 | 0.903829 |
| MA0039.2 | 1.10518 |
| MA0138.2 | 1.07027 |
| MA0002.2 | 0.466067 |
| MA0137.2 | 0.668025 |
| MA0104.2 | 0.48458 |
| MA0047.2 | 0.962424 |
| MA0112.2 | 0.29236 |
| MA0065.2 | 1.44804 |
| MA0150.1 | 0.784464 |
| MA0151.1 | 0 |
| MA0152.1 | 0.962542 |
| MA0153.1 | 1.43238 |
| MA0154.1 | 1.65374 |
| MA0155.1 | 0.840842 |
| MA0156.1 | 0.656895 |
| MA0157.1 | 1.12772 |
| MA0158.1 | 0 |
| MA0159.1 | 0.569393 |
| MA0160.1 | 0.823568 |
| MA0161.1 | 0 |
| MA0162.1 | 1.53682 |
| MA0163.1 | 2.12767 |
| MA0164.1 | 2.15144 |
| MA0080.2 | 0.64167 |
| MA0018.2 | 0.944669 |
| MA0099.2 | 1.06348 |
| MA0079.2 | 1.4764 |
| MA0102.2 | 2.01714 |
| MA0258.1 | 0.520639 |
| MA0259.1 | 0.543506 |
| MA0442.1 | 0 |
